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Ali A, Ahmad S, de Albuquerque PMM, Kamil A, Alshammari FA, Alouffi A, da Silva Vaz I. Prediction of Novel Drug Targets and Vaccine Candidates against Human Lice (Insecta), Acari (Arachnida), and Their Associated Pathogens. Vaccines (Basel) 2021; 10:vaccines10010008. [PMID: 35062669 PMCID: PMC8778234 DOI: 10.3390/vaccines10010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/12/2023] Open
Abstract
The emergence of drug-resistant lice, acari, and their associated pathogens (APs) is associated with economic losses; thus, it is essential to find new appropriate therapeutic approaches. In the present study, a subtractive proteomics approach was used to predict suitable therapeutics against these vectors and their infectious agents. We found 9701 proteins in the lice (Pediculus humanus var. corporis) and acari (Ixodes scapularis, Leptotrombidium deliense), and 4822 proteins in the proteomes of their APs (Babesia microti, Borreliella mayonii, Borrelia miyamotoi, Borrelia recurrentis, Rickettsia prowazekii, Orientia tsutsugamushi str. Boryong) that were non-homologous to host proteins. Among these non-homologous proteins, 365 proteins of lice and acari, and 630 proteins of APs, were predicted as essential proteins. Twelve unique essential proteins were predicted to be involved in four unique metabolic pathways of lice and acari, and 103 unique proteins were found to be involved in 75 unique metabolic pathways of APs. The sub cellular localization analysis of 115 unique essential proteins of lice and acari and their APs revealed that 61 proteins were cytoplasmic, 42 as membrane-bound proteins and 12 proteins with multiple localization. The druggability analysis of the identified 73 cytoplasmic and multiple localization essential proteins revealed 22 druggable targets and 51 novel drug targets that participate in unique pathways of lice and acari and their APs. Further, the predicted 42 membrane bound proteins could be potential vaccine candidates. Screening of useful inhibitors against these novel targets may result in finding novel compounds efficient for the control of these parasites.
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Affiliation(s)
- Abid Ali
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (S.A.); (P.M.M.d.A.)
| | - Shabir Ahmad
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (S.A.); (P.M.M.d.A.)
| | | | - Atif Kamil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan;
| | - Fahdah Ayed Alshammari
- College of Sciences and Literature Microbiology, Nothern Border University, Rafha 76413, Saudi Arabia;
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh 12354, Saudi Arabia;
- Vaccines Research for Infectious Diseases, King Saud University, Riyadh 11495, Saudi Arabia
- Veterinary Laboratories and Vaccines Center, Ministry of Environment Water & Agriculture, Riyadh 11195, Saudi Arabia
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil; (S.A.); (P.M.M.d.A.)
- Correspondence: ; Tel.: +55-(51)-33086078; Fax: +55-(51)-33087309
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Abstract
The ESKAPEE pathogens are the leading cause of health care-associated infections worldwide. Two-component systems (TCSs) can be used as effective targets against pathogenic bacteria since they are ubiquitous and manage various vital functions such as antibiotic resistance, virulence, biofilms, quorum sensing, and pH balance, among others. The two-component system (TCS) helps bacteria sense and respond to environmental stimuli through histidine kinases and response regulators. TCSs are the largest family of multistep signal transduction processes, and they are involved in many important cellular processes such as antibiotic resistance, pathogenicity, quorum sensing, osmotic stress, and biofilms. Here, we perform the first comprehensive study to highlight the role of TCSs as potential drug targets against ESKAPEE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli) pathogens through annotation, mapping, pangenomic status, gene orientation, and sequence variation analysis. The distribution of the TCSs is group specific with regard to Gram-positive and Gram-negative bacteria, except for KdpDE. The TCSs among ESKAPEE pathogens form closed pangenomes, except for Pseudomonas aeruginosa. Furthermore, their conserved nature due to closed pangenomes might make them good drug targets. Fitness score analysis suggests that any mutation in some TCSs such as BaeSR, ArcBA, EvgSA, and AtoSC, etc., might be lethal to the cell. Taken together, the results of this pangenomic assessment of TCSs reveal a range of strategies deployed by the ESKAPEE pathogens to manifest pathogenicity and antibiotic resistance. This study further suggests that the conserved features of TCSs might make them an attractive group of potential targets with which to address antibiotic resistance. IMPORTANCE The ESKAPEE pathogens are the leading cause of health care-associated infections worldwide. Two-component systems (TCSs) can be used as effective targets against pathogenic bacteria since they are ubiquitous and manage various vital functions such as antibiotic resistance, virulence, biofilms, quorum sensing, and pH balance, among others. This study provides a comprehensive overview of the pangenomic status of the TCSs among ESKAPEE pathogens. The annotation and pangenomic analysis of TCSs show that they are significantly distributed and conserved among the pathogens, as most of them form closed pangenomes. Furthermore, our analysis also reveals that the removal of the TCSs significantly affects the fitness of the cell. Hence, they may be used as promising drug targets against bacteria.
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Ali A, Ahmad S, Wadood A, Rehman AU, Zahid H, Qayash Khan M, Nawab J, Rahman ZU, Alouffi AS. Modeling Novel Putative Drugs and Vaccine Candidates against Tick-Borne Pathogens: A Subtractive Proteomics Approach. Vet Sci 2020; 7:E129. [PMID: 32906620 PMCID: PMC7557734 DOI: 10.3390/vetsci7030129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Ticks and tick-borne pathogens (TBPs) continuously causing substantial losses to the public and veterinary health sectors. The identification of putative drug targets and vaccine candidates is crucial to control TBPs. No information has been recorded on designing novel drug targets and vaccine candidates based on proteins. Subtractive proteomics is an in silico approach that utilizes extensive screening for the identification of novel drug targets or vaccine candidates based on the determination of potential target proteins available in a pathogen proteome that may be used effectively to control diseases caused by these infectious agents. The present study aimed to investigate novel drug targets and vaccine candidates by utilizing subtractive proteomics to scan the available proteomes of TBPs and predict essential and non-host homologous proteins required for the survival of these diseases causing agents. Subtractive proteome analysis revealed a list of fifteen essential, non-host homologous, and unique metabolic proteins in the complete proteome of selected pathogens. Among these therapeutic target proteins, three were excluded due to the presence in host gut metagenome, eleven were found to be highly potential drug targets, while only one was found as a potential vaccine candidate against TBPs. The present study may provide a foundation to design potential drug targets and vaccine candidates for the effective control of infections caused by TBPs.
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Affiliation(s)
- Abid Ali
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.A.); (S.A.); (H.Z.); (M.Q.K.)
| | - Shabir Ahmad
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.A.); (S.A.); (H.Z.); (M.Q.K.)
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.W.); (A.U.R.)
| | - Ashfaq U. Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.W.); (A.U.R.)
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hafsa Zahid
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.A.); (S.A.); (H.Z.); (M.Q.K.)
| | - Muhammad Qayash Khan
- Department of Zoology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan; (A.A.); (S.A.); (H.Z.); (M.Q.K.)
| | - Javed Nawab
- Department of Environmental Sciences, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan;
| | - Zia Ur Rahman
- Department of Microbiology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa 23200, Pakistan;
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Rahman N, Muhammad I, Nayab GE, Khan H, Filosa R, Xiao J, Hassan STS. In-silico Subtractive Proteomic Analysis Approach for Therapeutic Targets in MDR Salmonella enterica subsp. enterica serovar Typhi str. CT18. Curr Top Med Chem 2020; 19:2708-2717. [PMID: 31702501 DOI: 10.2174/1568026619666191105102156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/02/2019] [Accepted: 10/04/2019] [Indexed: 02/08/2023]
Abstract
OBJECTIVE In the present study, an attempt has been made for subtractive proteomic analysis approach for novel drug targets in Salmonella enterica subsp. enterica serover Typhi str.CT18 using computational tools. METHODS Paralogous, redundant and less than 100 amino acid protein sequences were removed by using CD-HIT. Further detection of bacterial proteins which are non-homologous to host and are essential for the survival of pathogens by using BLASTp against host proteome and DEG`s, respectively. Comparative Metabolic pathways analysis was performed to find unique and common metabolic pathways. The non-redundant, non-homologous and essential proteins were BLAST against approved drug targets for drug targets while Psortb and CELLO were used to predict subcellular localization. RESULTS There were 4473 protein sequences present in NCBI Database for Salmonella enterica subsp. enterica serover Typhi str. CT18 out of these 327 were essential proteins which were non-homologous to human. Among these essential proteins, 124 proteins were involved in 19 unique metabolic pathways. These proteins were further BLAST against approved drug targets in which 7 cytoplasmic proteins showed druggability and can be used as a therapeutic target. CONCLUSION Drug targets identification is the prime step towards drug discovery. We identified 7 cytoplasmic druggable proteins which are essential for the pathogen survival and non-homologous to human proteome. Further in vitro and in vivo validation is needed for the evaluation of these targets to combat against salmonellosis.
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Affiliation(s)
- Noor Rahman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Ijaz Muhammad
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Gul E Nayab
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan-23200, KP, Pakistan
| | - Rosanna Filosa
- Università della Campania Luigi Vanvitelli, Department of Environmental Biological and Pharmaceutical Sciences and Technologies, Naples, Italy.,Consorzio Sannio Tech-AMP Biotec, Appia Str. 7, 82030 Apollosa, BN, Italy
| | - Jianbo Xiao
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Control in Chinese Medicine, University of Macau, Taipa, Macao
| | - Sherif T S Hassan
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
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Tierney AR, Rather PN. Roles of two-component regulatory systems in antibiotic resistance. Future Microbiol 2019; 14:533-552. [PMID: 31066586 DOI: 10.2217/fmb-2019-0002] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Two-component regulatory systems (TCSs) are a major mechanism by which bacteria sense and respond to changes in their environment. TCSs typically consist of two proteins that bring about major regulation of the cell genome through coordinated action mediated by phosphorylation. Environmental conditions that activate TCSs are numerous and diverse and include exposure to antibiotics as well as conditions inside a host. The resulting regulatory action often involves activation of antibiotic defenses and changes to cell physiology that increase antibiotic resistance. Examples of resistance mechanisms enacted by TCSs contained in this review span those found in both Gram-negative and Gram-positive species and include cell surface modifications, changes in cell permeability, increased biofilm formation, and upregulation of antibiotic-degrading enzymes.
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Affiliation(s)
- Aimee Rp Tierney
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, 30322 USA
| | - Philip N Rather
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA, 30322 USA.,Research Service, Department of Veterans' Affairs, Atlanta VA Health Care System, Decatur, GA, 30033 USA
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Wadood A, Ghufran M, Khan A, Azam SS, Uddin R, Waqas M, Saleem S. The methicillin-resistant S. epidermidis strain RP62A genome mining for potential novel drug targets identification. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Sivakumar D, Lahiri C, Chakravortty D. Computational studies on histidine kinase protein BaeS to target multidrug-resistant Salmonella. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0188-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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In silico identification of common putative drug targets in Leptospira interrogans. J Chem Biol 2010; 3:165-73. [PMID: 21572503 DOI: 10.1007/s12154-010-0039-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Accepted: 04/22/2010] [Indexed: 10/19/2022] Open
Abstract
Infectious diseases are the leading causes of death worldwide. Hence, there is a need to develop new antimicrobial agents. Traditional method of drug discovery is time consuming and yields a few drug targets with little intracellular information for guiding target selection. Thus, focus in drug development has been shifted to computational comparative genomics for identifying novel drug targets. Leptospirosis is a worldwide zoonosis of global concern caused by Leptospira interrogans. Availability of L. interrogans serovars and human genome sequences facilitated to search for novel drug targets using bioinformatics tools. The genome sequence of L. interrogans serovar Copenhageni has 5,124 genes while that of serovar Lai has 4,727 genes. Through subtractive genomic approach 218 genes in serovar Copenhageni and 158 genes in serovar Lai have been identified as putative drug targets. Comparative genomic approach had revealed that 88 drug targets were common to both the serovars. Pathway analysis using the Kyoto Encyclopaedia of Genes and Genomes revealed that 66 targets are enzymes and 22 are non-enzymes. Sixty two common drug targets were predicted to be localized in cytoplasm and 16 were surface proteins. The identified potential drug targets form a platform for further investigation in discovery of novel therapeutic compounds against Leptospira.
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